Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001253.1 Hibiscus syriacus cultivar Beakdansim tig00002459_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 107878
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.34
Found at i:78 original size:44 final size:45
Alignment explanation
Indices: 1--283 Score: 306
Period size: 44 Copynumber: 6.4 Consensus size: 45
* * *
1 GATGCCATAAATGAAATGCATAAC-ATGCATTATCGACATGAAAG
1 GATGCCATAAATGAAATACATAACGGTGCATTATCGGCATGAAAG
** ** *
45 GATGTTATAAATGAAATACAT-ACGGTGTGTTATCGGCATGAAAT
1 GATGCCATAAATGAAATACATAACGGTGCATTATCGGCATGAAAG
* * * *
89 GAGGCCAT-AACGAAATGCATAACGATGCATTATCGGCATGAAAG
1 GATGCCATAAATGAAATACATAACGGTGCATTATCGGCATGAAAG
* * * *
133 GATGCCATAAAT-AAATGCATAATGGTGCATTATTGGCATGAAAA
1 GATGCCATAAATGAAATACATAACGGTGCATTATCGGCATGAAAG
*
177 AATGCCATAAATGAAATGA-ATAACGGTGCATTATCGGCATGAAAG
1 GATGCCATAAATGAAAT-ACATAACGGTGCATTATCGGCATGAAAG
* * ** *
222 GATGCCATAAATGAAAAGACATAATGGTGCATTATAAGCATGAAAT
1 GATGCCATAAATG-AAATACATAACGGTGCATTATCGGCATGAAAG
*
268 GATGCTATAAATGAAA
1 GATGCCATAAATGAAA
284 ATAAATGATA
Statistics
Matches: 197, Mismatches: 35, Indels: 13
0.80 0.14 0.05
Matches are distributed among these distances:
43 12 0.06
44 103 0.52
45 45 0.23
46 37 0.19
ACGTcount: A:0.42, C:0.13, G:0.21, T:0.24
Consensus pattern (45 bp):
GATGCCATAAATGAAATACATAACGGTGCATTATCGGCATGAAAG
Found at i:171 original size:88 final size:90
Alignment explanation
Indices: 4--283 Score: 352
Period size: 88 Copynumber: 3.1 Consensus size: 90
1 GAT
* ** *
4 GCCATAAATGAAATGCATAAC-ATGCATTATCGACATGAAAGGATGTTATAAATGAAATACAT-A
1 GCCATAAATGAAATGCATAACGATGCATTATCGGCATGAAAGGATGCCATAAATGAAATGCATAA
* ** *
67 CGGTGTGTTATCGGCATGAAATGAG
66 TGGTGCATTATAGGCATGAAATGAG
*
92 GCCAT-AACGAAATGCATAACGATGCATTATCGGCATGAAAGGATGCCATAAAT-AAATGCATAA
1 GCCATAAATGAAATGCATAACGATGCATTATCGGCATGAAAGGATGCCATAAATGAAATGCATAA
* ** *
155 TGGTGCATTATTGGCATGAAAAAAT
66 TGGTGCATTATAGGCATGAAATGAG
* * *
180 GCCATAAATGAAATGAATAACGGTGCATTATCGGCATGAAAGGATGCCATAAATGAAAAGACATA
1 GCCATAAATGAAATGCATAACGATGCATTATCGGCATGAAAGGATGCCATAAATGAAATG-CATA
* *
245 ATGGTGCATTATAAGCATGAAATGAT
65 ATGGTGCATTATAGGCATGAAATGAG
*
271 GCTATAAATGAAA
1 GCCATAAATGAAA
284 ATAAATGATA
Statistics
Matches: 166, Mismatches: 21, Indels: 7
0.86 0.11 0.04
Matches are distributed among these distances:
87 21 0.13
88 58 0.35
89 45 0.27
90 4 0.02
91 38 0.23
ACGTcount: A:0.42, C:0.13, G:0.21, T:0.24
Consensus pattern (90 bp):
GCCATAAATGAAATGCATAACGATGCATTATCGGCATGAAAGGATGCCATAAATGAAATGCATAA
TGGTGCATTATAGGCATGAAATGAG
Found at i:1424 original size:18 final size:19
Alignment explanation
Indices: 1401--1456 Score: 69
Period size: 21 Copynumber: 2.9 Consensus size: 19
1391 TGTAATCTTT
1401 TGAAAATACATGA-TTTAA
1 TGAAAATACATGATTTTAA
1419 TGAAAATACATGAGTTTTTAA
1 TGAAAATACATGA--TTTTAA
* *
1440 TGAAAGTACATGCTTTT
1 TGAAAATACATGATTTT
1457 GGATGAATGA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
18 13 0.39
19 4 0.12
21 16 0.48
ACGTcount: A:0.41, C:0.07, G:0.14, T:0.38
Consensus pattern (19 bp):
TGAAAATACATGATTTTAA
Found at i:1848 original size:17 final size:17
Alignment explanation
Indices: 1826--1880 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 17
1816 AACGTTCAGG
1826 AAAGGCACTTATTCTGA
1 AAAGGCACTTATTCTGA
* * *
1843 AAAGGCACGT-CT-TGG
1 AAAGGCACTTATTCTGA
*
1858 AAAGACACTTATTCTCGA
1 AAAGGCACTTATTCT-GA
1876 AAAGG
1 AAAGG
1881 AACGATTTAT
Statistics
Matches: 27, Mismatches: 8, Indels: 5
0.68 0.20 0.12
Matches are distributed among these distances:
15 10 0.37
16 2 0.07
17 10 0.37
18 5 0.19
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.24
Consensus pattern (17 bp):
AAAGGCACTTATTCTGA
Found at i:3466 original size:15 final size:15
Alignment explanation
Indices: 3443--3496 Score: 56
Period size: 15 Copynumber: 3.7 Consensus size: 15
3433 TTTAAACCAA
*
3443 TTTTTATTTCAAACC
1 TTTTAATTTCAAACC
*
3458 TTTTAATTTC-AACA
1 TTTTAATTTCAAACC
**
3472 TTTTAATTTCAGTCC
1 TTTTAATTTCAAACC
*
3487 TTTAAATTTC
1 TTTTAATTTC
3497 TAGTATTTCA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
14 13 0.41
15 19 0.59
ACGTcount: A:0.28, C:0.17, G:0.02, T:0.54
Consensus pattern (15 bp):
TTTTAATTTCAAACC
Found at i:3475 original size:14 final size:14
Alignment explanation
Indices: 3442--3482 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
3432 TTTTAAACCA
*
3442 ATTTTTATTTCAAAC
1 ATTTTAATTTC-AAC
*
3457 CTTTTAATTTCAAC
1 ATTTTAATTTCAAC
3471 ATTTTAATTTCA
1 ATTTTAATTTCA
3483 GTCCTTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
14 14 0.61
15 9 0.39
ACGTcount: A:0.32, C:0.15, G:0.00, T:0.54
Consensus pattern (14 bp):
ATTTTAATTTCAAC
Found at i:4050 original size:138 final size:138
Alignment explanation
Indices: 3830--4140 Score: 496
Period size: 138 Copynumber: 2.2 Consensus size: 138
3820 AATAATTTGT
* * * *
3830 TAAAATTGGTTAGGATTAGTATTAGAGCCTTCATTTTAGATTAATTTCATCGTTAGTCCTTTAAT
1 TAAAATTGATTAGGATTAATATTAGAGCCTTGA-TTTAGATTAATATCATCGTTAGTCCTTTAAT
* **
3895 TTAGGAGATTTTTTAATTTAGTCCTCACTTATATGCCTGAGATTCCATTTTAACTATTTGATTCA
65 TTAGGAGAATTTTTAATTTAGTCCTCACTTATATGCCCCAGATTCCATTTTAACTATTTGATTCA
3960 ATAAATGGA
130 ATAAATGGA
* * * *
3969 TAAATTTGATTAGGATTAATATTAGAGCCTTGATTTATATTAATATCATCTTTGGTCCTTTAATT
1 TAAAATTGATTAGGATTAATATTAGAGCCTTGATTTAGATTAATATCATCGTTAGTCCTTTAATT
*
4034 TAGGAGAATTTTTAATTTAGTCCTCACTTTTATGCCCCAGATTCCATTTTAACTATTTGATTCAA
66 TAGGAGAATTTTTAATTTAGTCCTCACTTATATGCCCCAGATTCCATTTTAACTATTTGATTCAA
*
4099 TAAATGGC
131 TAAATGGA
4107 TAAAATTGATTAGGATTAATATTAGAGCCTTGAT
1 TAAAATTGATTAGGATTAATATTAGAGCCTTGAT
4141 CTTTGGTCCT
Statistics
Matches: 158, Mismatches: 14, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
138 129 0.82
139 29 0.18
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.43
Consensus pattern (138 bp):
TAAAATTGATTAGGATTAATATTAGAGCCTTGATTTAGATTAATATCATCGTTAGTCCTTTAATT
TAGGAGAATTTTTAATTTAGTCCTCACTTATATGCCCCAGATTCCATTTTAACTATTTGATTCAA
TAAATGGA
Found at i:5774 original size:24 final size:22
Alignment explanation
Indices: 5750--5833 Score: 68
Period size: 24 Copynumber: 3.8 Consensus size: 22
5740 TTTTAATAAT
5750 TTAATATAATTTATATATTAAAA
1 TTAATA-AATTTATATATTAAAA
*
5773 TTAA-AAA-TGATATATT--AA
1 TTAATAAATTTATATATTAAAA
*
5791 TTATACTAATTTTATATATTATAATA
1 TTA-A-TAAATTTATATATTA-AA-A
*
5817 TTAATAAATTTAAATAT
1 TTAATAAATTTATATAT
5834 AATTTAAGTT
Statistics
Matches: 48, Mismatches: 5, Indels: 15
0.71 0.07 0.22
Matches are distributed among these distances:
18 5 0.10
19 1 0.02
20 8 0.17
21 4 0.08
22 9 0.19
23 4 0.08
24 11 0.23
25 2 0.04
26 4 0.08
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (22 bp):
TTAATAAATTTATATATTAAAA
Found at i:6085 original size:18 final size:18
Alignment explanation
Indices: 6062--6116 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
6052 AAAGGTTAAG
6062 ATTTAAATTAATATCTAA
1 ATTTAAATTAATATCTAA
6080 ATTT-AATT--TAT-T-A
1 ATTTAAATTAATATCTAA
6093 ATTTAAATTAATA-CATAA
1 ATTTAAATTAATATC-TAA
6111 ATTTAA
1 ATTTAA
6117 CTTTTTATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 12
0.72 0.00 0.28
Matches are distributed among these distances:
13 5 0.16
14 5 0.16
15 3 0.10
16 2 0.06
17 5 0.16
18 11 0.35
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (18 bp):
ATTTAAATTAATATCTAA
Found at i:6097 original size:31 final size:30
Alignment explanation
Indices: 6062--6129 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 30
6052 AAAGGTTAAG
6062 ATTTAAATTAATATC-TAAATTTAA-TTTATT
1 ATTTAAATTAATA-CATAAATTTAACTTT-TT
6092 AATTTAAATTAATACATAAATTTAACTTTTT
1 -ATTTAAATTAATACATAAATTTAACTTTTT
6123 ATTTAAA
1 ATTTAAA
6130 ATAAATATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
30 8 0.23
31 24 0.69
32 3 0.09
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (30 bp):
ATTTAAATTAATACATAAATTTAACTTTTT
Found at i:6237 original size:2 final size:2
Alignment explanation
Indices: 6230--6299 Score: 80
Period size: 2 Copynumber: 38.0 Consensus size: 2
6220 GTTAGGATTA
*
6230 AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AA AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
6270 AT AT -T AT -T AT AT AT AT -T AT AT TT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6300 TTATTATCAA
Statistics
Matches: 58, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
1 6 0.10
2 52 0.90
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:6255 original size:21 final size:21
Alignment explanation
Indices: 6231--6299 Score: 95
Period size: 21 Copynumber: 3.2 Consensus size: 21
6221 TTAGGATTAA
6231 TATATATATATATATATATAT
1 TATATATATATATATATATAT
*
6252 TATATATATAAATATATTATAT
1 TATATATATATATATA-TATAT
*
6274 TAT-TATATATATTATATTTAT
1 TATATATATATA-TATATATAT
6295 TATAT
1 TATAT
6300 TTATTATCAA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
21 29 0.69
22 13 0.31
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TATATATATATATATATATAT
Found at i:6257 original size:17 final size:18
Alignment explanation
Indices: 6226--6306 Score: 100
Period size: 17 Copynumber: 4.8 Consensus size: 18
6216 TTATGTTAGG
6226 ATTA-ATATA-TATATAT
1 ATTATATATATTATATAT
6242 A-TATATATATTATATAT
1 ATTATATATATTATATAT
*
6259 A-TAAATATATTATAT-T
1 ATTATATATATTATATAT
*
6275 ATTATATATATTATATTT
1 ATTATATATATTATATAT
*
6293 ATTATATTTATTAT
1 ATTATATATATTAT
6307 CAATTAACAA
Statistics
Matches: 58, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
15 2 0.03
16 8 0.14
17 34 0.59
18 14 0.24
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTATATATATTATATAT
Found at i:6300 original size:23 final size:23
Alignment explanation
Indices: 6230--6300 Score: 74
Period size: 25 Copynumber: 3.0 Consensus size: 23
6220 GTTAGGATTA
*
6230 ATATATA-TATATATATATATATT
1 ATATATATTATATTTAT-TATATT
*
6253 ATATATATAAATATATTA-TATTATT
1 ATATATAT-TATAT-TTATTA-TATT
6278 ATATATATTATATTTATTATATT
1 ATATATATTATATTTATTATATT
6301 TATTATCAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
23 14 0.35
24 8 0.20
25 16 0.40
26 2 0.05
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
ATATATATTATATTTATTATATT
Found at i:7825 original size:23 final size:23
Alignment explanation
Indices: 7782--7825 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
7772 ACATTTTATG
*
7782 GCACATATGTGATATTTGTGCTT
1 GCACATATGTGATATTGGTGCTT
*
7805 GCACGTATGTGATGA-TGGTGC
1 GCACATATGTGAT-ATTGGTGC
7826 AATGTATTCC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 17 0.94
24 1 0.06
ACGTcount: A:0.20, C:0.14, G:0.30, T:0.36
Consensus pattern (23 bp):
GCACATATGTGATATTGGTGCTT
Found at i:8170 original size:34 final size:33
Alignment explanation
Indices: 8132--8201 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 33
8122 AAAAAATTAG
*
8132 TGATTTAAATGAA-TGTGAAAAGTACATGATTATA
1 TGATTTAAA-CAATTGTGAAAAGTACATG-TTATA
* *
8166 TGATTTGAACAATTGTGAAAAGTGCATGTTATA
1 TGATTTAAACAATTGTGAAAAGTACATGTTATA
8199 TGA
1 TGA
8202 CATGAATACT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
33 10 0.31
34 22 0.69
ACGTcount: A:0.40, C:0.04, G:0.20, T:0.36
Consensus pattern (33 bp):
TGATTTAAACAATTGTGAAAAGTACATGTTATA
Found at i:26037 original size:31 final size:31
Alignment explanation
Indices: 26002--26062 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
25992 AATACAGTCC
*
26002 CCCAACATTTAGTAT-GTTTGCAATATGGTCT
1 CCCAACATTTAGT-TCATTTGCAATATGGTCT
26033 CCCAACATTTAGTTCATTTGCAATATGGTC
1 CCCAACATTTAGTTCATTTGCAATATGGTC
26063 CCCGATGTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
30 1 0.04
31 27 0.96
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (31 bp):
CCCAACATTTAGTTCATTTGCAATATGGTCT
Found at i:27417 original size:23 final size:23
Alignment explanation
Indices: 27387--27436 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
27377 GAGCAACAAG
27387 CAACAGATCACCTGATATGAACC
1 CAACAGATCACCTGATATGAACC
27410 CAACAGATCACCTGATATGAACC
1 CAACAGATCACCTGATATGAACC
27433 CAAC
1 CAAC
27437 TGACGCGCAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.40, C:0.32, G:0.12, T:0.16
Consensus pattern (23 bp):
CAACAGATCACCTGATATGAACC
Found at i:38606 original size:20 final size:20
Alignment explanation
Indices: 38583--38692 Score: 184
Period size: 20 Copynumber: 5.5 Consensus size: 20
38573 GGCCATACAA
38583 TATCGATACTGCCTGTCGGG
1 TATCGATACTGCCTGTCGGG
38603 TATCGATACTGCCTGTCGGG
1 TATCGATACTGCCTGTCGGG
**
38623 TATCGATACTGTGTGTCGGG
1 TATCGATACTGCCTGTCGGG
*
38643 TATCGATATTGCCTGTCGGG
1 TATCGATACTGCCTGTCGGG
*
38663 TATAGATACTGCCTGTCGGG
1 TATCGATACTGCCTGTCGGG
38683 TATCGATACT
1 TATCGATACT
38693 TTTTCCCAGG
Statistics
Matches: 82, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 82 1.00
ACGTcount: A:0.17, C:0.21, G:0.29, T:0.33
Consensus pattern (20 bp):
TATCGATACTGCCTGTCGGG
Found at i:38633 original size:60 final size:60
Alignment explanation
Indices: 38561--38692 Score: 178
Period size: 60 Copynumber: 2.2 Consensus size: 60
38551 ATAACTCATT
*
38561 GGTATCGATACTG-GCCATAC-AATATCGATACTGCCTGTCGGGTATCGATACTGCCTGTCG
1 GGTATCGATACTGTG-CAT-CGAATATCGATACTGCCTGTCGGGTATAGATACTGCCTGTCG
** ** *
38621 GGTATCGATACTGTGTGTCGGGTATCGATATTGCCTGTCGGGTATAGATACTGCCTGTCG
1 GGTATCGATACTGTGCATCGAATATCGATACTGCCTGTCGGGTATAGATACTGCCTGTCG
38681 GGTATCGATACT
1 GGTATCGATACT
38693 TTTTCCCAGG
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
59 1 0.02
60 62 0.97
61 1 0.02
ACGTcount: A:0.20, C:0.21, G:0.28, T:0.31
Consensus pattern (60 bp):
GGTATCGATACTGTGCATCGAATATCGATACTGCCTGTCGGGTATAGATACTGCCTGTCG
Found at i:38705 original size:60 final size:60
Alignment explanation
Indices: 38583--38712 Score: 197
Period size: 60 Copynumber: 2.2 Consensus size: 60
38573 GGCCATACAA
* ** *
38583 TATCGATACTGCCTGTCGGGTATCGATACTGCCTGTCGGGTATCGATACTGTGTGTCGGG
1 TATCGATACTGCCTGTCGGGTATAGATACTGCCTGTCGGGTATCGATACTGTGTCCCAGG
* * *
38643 TATCGATATTGCCTGTCGGGTATAGATACTGCCTGTCGGGTATCGATACTTTTTCCCAGG
1 TATCGATACTGCCTGTCGGGTATAGATACTGCCTGTCGGGTATCGATACTGTGTCCCAGG
38703 TATCGATACT
1 TATCGATACT
38713 TCAATGCATA
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 62 1.00
ACGTcount: A:0.18, C:0.22, G:0.27, T:0.34
Consensus pattern (60 bp):
TATCGATACTGCCTGTCGGGTATAGATACTGCCTGTCGGGTATCGATACTGTGTCCCAGG
Found at i:40528 original size:2 final size:2
Alignment explanation
Indices: 40521--40551 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
40511 TGGATAAGAA
*
40521 AG AG AG AG AG AA AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
40552 TTTGAAAGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:40534 original size:12 final size:12
Alignment explanation
Indices: 40517--40551 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
40507 AGAATGGATA
40517 AGAAAGAGAGAG
1 AGAAAGAGAGAG
40529 AGAAAGAGAGAG
1 AGAAAGAGAGAG
*
40541 AGAGAGAGAGA
1 AGAAAGAGAGA
40552 TTTGAAAGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (12 bp):
AGAAAGAGAGAG
Found at i:44215 original size:23 final size:25
Alignment explanation
Indices: 44154--44223 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 25
44144 TGAAAGGAAG
44154 AAAAAGGGAGAAAATATGACAAATTT
1 AAAAAGGGAGAAAATA-GACAAATTT
** * *
44180 -AAAAGTAAAAAAATA-A-AATTTT
1 AAAAAGGGAGAAAATAGACAAATTT
44202 AAAAAGGGAGAAAATATGACAA
1 AAAAAGGGAGAAAATA-GACAA
44224 CTTTCATGTT
Statistics
Matches: 33, Mismatches: 7, Indels: 8
0.69 0.15 0.17
Matches are distributed among these distances:
22 5 0.15
23 13 0.39
25 13 0.39
26 2 0.06
ACGTcount: A:0.63, C:0.03, G:0.16, T:0.19
Consensus pattern (25 bp):
AAAAAGGGAGAAAATAGACAAATTT
Found at i:45284 original size:21 final size:20
Alignment explanation
Indices: 45245--45291 Score: 67
Period size: 21 Copynumber: 2.3 Consensus size: 20
45235 TAAATGTAAA
*
45245 TATAATTTAAATATTATATT
1 TATAATTTAAATATAATATT
*
45265 TTTAATTTACAATATAATATT
1 TATAATTTA-AATATAATATT
45286 TATAAT
1 TATAAT
45292 AGATATTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (20 bp):
TATAATTTAAATATAATATT
Found at i:49602 original size:25 final size:25
Alignment explanation
Indices: 49574--49623 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
49564 TTTTATTGAG
49574 CTGTTACAGGTTTAATGCAAGAGTT
1 CTGTTACAGGTTTAATGCAAGAGTT
49599 CTGTTACAGGTTTAATGCAAGAGTT
1 CTGTTACAGGTTTAATGCAAGAGTT
49624 ACAAAACTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.12, G:0.24, T:0.36
Consensus pattern (25 bp):
CTGTTACAGGTTTAATGCAAGAGTT
Found at i:49639 original size:22 final size:21
Alignment explanation
Indices: 49609--49672 Score: 76
Period size: 22 Copynumber: 3.0 Consensus size: 21
49599 CTGTTACAGG
*
49609 TTTAATGCAAGAGTTACAAAA
1 TTTATTGCAAGAGTTACAAAA
*
49630 CTTTATTGCAAGAGTTACATAGA
1 -TTTATTGCAAGAGTTACA-AAA
49653 TTTATTG-AATGAGTTACAAA
1 TTTATTGCAA-GAGTTACAAA
49673 GTGCTGGATT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
21 3 0.08
22 32 0.86
23 2 0.05
ACGTcount: A:0.41, C:0.09, G:0.16, T:0.34
Consensus pattern (21 bp):
TTTATTGCAAGAGTTACAAAA
Found at i:51761 original size:20 final size:20
Alignment explanation
Indices: 51738--51789 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
51728 CGGCAAAGAG
51738 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
51758 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
51778 CATGTATTTTCA
1 CATGTATTTTCA
51790 AAGGGGTTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.37, C:0.15, G:0.06, T:0.42
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:64010 original size:3 final size:3
Alignment explanation
Indices: 63999--64037 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
63989 CCCTTTTTTT
*
63999 TTA TATA TTA TTA TTA TTA -TA TTA TTG TTA TTA TTA TTA
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
64038 ATTAAGTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.06
3 27 0.84
4 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:64021 original size:14 final size:14
Alignment explanation
Indices: 64002--64037 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
63992 TTTTTTTTTA
64002 TATATTATTATTAT
1 TATATTATTATTAT
*
64016 TATATTATTGTTAT
1 TATATTATTATTAT
64030 TATTATTA
1 TA-TATTA
64038 ATTAAGTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 15 0.75
15 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (14 bp):
TATATTATTATTAT
Found at i:66224 original size:131 final size:129
Alignment explanation
Indices: 65932--66270 Score: 410
Period size: 131 Copynumber: 2.6 Consensus size: 129
65922 ATTTTGATCA
* * * * * * *
65932 GAGTAATAAATGACTGCTTTCAGGCATAAGAGGTCATTTATTCTCGATTGGAAATAATTTGATAT
1 GAGTAATAAATGAATGTTTTAATGCACAAAAGGTCATTTATTCTCGATTGGAAATAATTAGATAT
* * * * * **
65997 TGTCATTTTCTCTCGAATTAATATCGATTTTTTAGACGGAATATTTATCTCTTTATTTCAATTG
66 TATCATTTTCACTCGAATTAATATCGAATTTTAAGACGAAATATACATCTCTTTATTTCAATTG
* * * * * *
66061 GGGTAACAAAT-AATTGTTTTAATGCACGAAAGGTCATTTATTCTTGATTGGAAATCATTAGATG
1 GAGTAATAAATGAA-TGTTTTAATGCACAAAAGGTCATTTATTCTCGATTGGAAATAATTAGATA
* * * * *
66125 TTATTATTTTCACTTGAATTGATATTGAATTTTAAGATGAAATAGTAACATCTCTTTATTTCAAT
65 TTATCATTTTCACTCGAATTAATATCGAATTTTAAGACGAAATA-T-ACATCTCTTTATTTCAAT
66190 TG
128 TG
66192 GAGTAATAAATGAATGTTTTAATGCACAAAAGGTCATTTATTCTCGATTGGAAATAATTAGATAT
1 GAGTAATAAATGAATGTTTTAATGCACAAAAGGTCATTTATTCTCGATTGGAAATAATTAGATAT
*
66257 TATCGTTTTCACTC
66 TATCATTTTCACTC
66271 TTAAAATTAT
Statistics
Matches: 172, Mismatches: 34, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
128 1 0.01
129 83 0.48
130 1 0.01
131 85 0.49
132 2 0.01
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.41
Consensus pattern (129 bp):
GAGTAATAAATGAATGTTTTAATGCACAAAAGGTCATTTATTCTCGATTGGAAATAATTAGATAT
TATCATTTTCACTCGAATTAATATCGAATTTTAAGACGAAATATACATCTCTTTATTTCAATTG
Found at i:69307 original size:2 final size:2
Alignment explanation
Indices: 69300--69329 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
69290 ATCCCTTCAA
69300 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
69330 CCCTTGTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:69626 original size:13 final size:12
Alignment explanation
Indices: 69599--69629 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
69589 AAAAACACAC
69599 AAAAAATTAAAG
1 AAAAAATTAAAG
69611 AAAAAATTAAAG
1 AAAAAATTAAAG
*
69623 GAAAAAT
1 AAAAAAT
69630 AGAAAAAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.10, T:0.16
Consensus pattern (12 bp):
AAAAAATTAAAG
Found at i:69639 original size:28 final size:29
Alignment explanation
Indices: 69607--69669 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 29
69597 ACAAAAAATT
* * *
69607 AAAGAAAAAATTA-AAGGAAAAATAGAAA
1 AAAGAAAAAATAAGAAAGAAAAAAAGAAA
69635 AAAG-AAAAATAAGAAAGAAAAAAAGAAA
1 AAAGAAAAAATAAGAAAGAAAAAAAGAAA
*
69663 GAAGAAA
1 AAAGAAA
69670 GGAAACAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 7 0.24
28 20 0.69
29 2 0.07
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.06
Consensus pattern (29 bp):
AAAGAAAAAATAAGAAAGAAAAAAAGAAA
Found at i:69643 original size:15 final size:15
Alignment explanation
Indices: 69623--69669 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
69613 AAAATTAAAG
69623 GAAAAATAGAAAAAA
1 GAAAAATAGAAAAAA
*
69638 GAAAAAT--AAGAAA
1 GAAAAATAGAAAAAA
* *
69651 GAAAAAAAGAAAGAA
1 GAAAAATAGAAAAAA
69666 GAAA
1 GAAA
69670 GGAAACAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
13 11 0.42
15 15 0.58
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (15 bp):
GAAAAATAGAAAAAA
Found at i:69660 original size:12 final size:13
Alignment explanation
Indices: 69635--69665 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
69625 AAAATAGAAA
69635 AAAGAAAAATAAG
1 AAAGAAAAATAAG
69648 AAAGAAAAA-AAG
1 AAAGAAAAATAAG
69660 AAAGAA
1 AAAGAA
69666 GAAAGGAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 9 0.50
13 9 0.50
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (13 bp):
AAAGAAAAATAAG
Found at i:71341 original size:40 final size:40
Alignment explanation
Indices: 71282--71483 Score: 368
Period size: 40 Copynumber: 5.0 Consensus size: 40
71272 ACCATAGTGC
71282 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
* *
71322 TACACATAAGGTTGCGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
71362 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
71402 TACACATAAGGTCGTGCCCACCATATATACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
71442 TACACATAAGGTCGTGCCCACCATATGCACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
71482 TA
1 TA
71484 TAAACATGCA
Statistics
Matches: 155, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 155 1.00
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.23
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:75430 original size:17 final size:17
Alignment explanation
Indices: 75408--75481 Score: 98
Period size: 17 Copynumber: 4.4 Consensus size: 17
75398 CAAGTGAAAT
75408 ATTTTTTT-TCATTTCTC
1 ATTTTTTTCTCATTT-TC
75425 ATTTTTTTCTCATTTTC
1 ATTTTTTTCTCATTTTC
*
75442 TTTTTTTTCTCATTTTC
1 ATTTTTTTCTCATTTTC
*
75459 ATTTTTTTCTTCGTTTTC
1 ATTTTTTTC-TCATTTTC
75477 -TTTTT
1 ATTTTT
75482 CTTTTTCTAT
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
17 39 0.75
18 13 0.25
ACGTcount: A:0.08, C:0.16, G:0.01, T:0.74
Consensus pattern (17 bp):
ATTTTTTTCTCATTTTC
Found at i:75430 original size:18 final size:17
Alignment explanation
Indices: 75409--75494 Score: 93
Period size: 18 Copynumber: 4.8 Consensus size: 17
75399 AAGTGAAATA
75409 TTTTTTTTCATTTCTCAT
1 TTTTTTTTCATTT-TCAT
*
75427 TTTTTTCTCATTTTC-T
1 TTTTTTTTCATTTTCAT
75443 TTTTTTTCTCATTTTCAT
1 TTTTTTT-TCATTTTCAT
* *
75461 TTTTTTCTTCGTTTTCTT
1 TTTTTT-TTCATTTTCAT
75479 TTTCTTTTTCTATTTT
1 TTT-TTTTTC-ATTTT
75495 TTTTCTTCTT
Statistics
Matches: 58, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
16 7 0.12
17 10 0.17
18 33 0.57
19 8 0.14
ACGTcount: A:0.07, C:0.16, G:0.01, T:0.76
Consensus pattern (17 bp):
TTTTTTTTCATTTTCAT
Found at i:75455 original size:35 final size:34
Alignment explanation
Indices: 75409--75486 Score: 113
Period size: 35 Copynumber: 2.2 Consensus size: 34
75399 AAGTGAAATA
75409 TTTTTTTTCATTTCTCATTTTTTTC-TCATTTTCT
1 TTTTTTTTCATTT-TCATTTTTTTCTTCATTTTCT
*
75443 TTTTTTTCTCATTTTCATTTTTTTCTTCGTTTTCT
1 TTTTTTT-TCATTTTCATTTTTTTCTTCATTTTCT
75478 TTTTCTTTT
1 TTTT-TTTT
75487 TCTATTTTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
34 18 0.45
35 19 0.47
36 3 0.08
ACGTcount: A:0.06, C:0.17, G:0.01, T:0.76
Consensus pattern (34 bp):
TTTTTTTTCATTTTCATTTTTTTCTTCATTTTCT
Found at i:75494 original size:7 final size:6
Alignment explanation
Indices: 75437--75519 Score: 66
Period size: 6 Copynumber: 14.2 Consensus size: 6
75427 TTTTTTCTCA
* * * *
75437 TTTTCT TTTT-T TTCTCA TTTTCAT TTTT-T TCTTCG TTTTCT TTTTCT
1 TTTTCT TTTTCT TTTTCT TTTTC-T TTTTCT TTTTCT TTTTCT TTTTCT
* *
75484 TTTTCT ATTT-T TTTTCT TCTTCT GTTTT-T TTTTCT T
1 TTTTCT TTTTCT TTTTCT TTTTCT -TTTTCT TTTTCT T
75520 ATAATATATA
Statistics
Matches: 59, Mismatches: 12, Indels: 12
0.71 0.14 0.14
Matches are distributed among these distances:
5 16 0.27
6 36 0.61
7 7 0.12
ACGTcount: A:0.04, C:0.16, G:0.02, T:0.78
Consensus pattern (6 bp):
TTTTCT
Found at i:75494 original size:29 final size:29
Alignment explanation
Indices: 75462--75518 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
75452 CATTTTCATT
75462 TTTTTCTTCGTT-TTCT-TTTTCTTTTTCTA
1 TTTTTCTTC-TTCTTCTGTTTT-TTTTTCTA
*
75491 TTTTTTTTCTTCTTCTGTTTTTTTTTCT
1 TTTTTCTTCTTCTTCTGTTTTTTTTTCT
75519 TATAATATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 2 0.08
29 19 0.76
30 4 0.16
ACGTcount: A:0.02, C:0.16, G:0.04, T:0.79
Consensus pattern (29 bp):
TTTTTCTTCTTCTTCTGTTTTTTTTTCTA
Found at i:75497 original size:17 final size:17
Alignment explanation
Indices: 75407--75515 Score: 77
Period size: 17 Copynumber: 6.6 Consensus size: 17
75397 ACAAGTGAAA
*
75407 TATTTTTTTTC-ATTTC
1 TATTTTTTTTCTTTTTC
*
75423 TCATTTTTTTCTCATTTTC
1 T-ATTTTTTT-TCTTTTTC
*
75442 T-TTTTTTTCTCATTTTC
1 TATTTTTTT-TCTTTTTC
**
75459 -A-TTTTTTTCTTCGT-
1 TATTTTTTTTCTTTTTC
*
75473 T-TTCTTTTTCTTTTTC
1 TATTTTTTTTCTTTTTC
*
75489 TATTTTTTTTCTTCTTC
1 TATTTTTTTTCTTTTTC
*
75506 TGTTTTTTTT
1 TATTTTTTTT
75516 TCTTATAATA
Statistics
Matches: 75, Mismatches: 10, Indels: 15
0.75 0.10 0.15
Matches are distributed among these distances:
15 14 0.19
16 8 0.11
17 46 0.61
18 2 0.03
19 5 0.07
ACGTcount: A:0.06, C:0.16, G:0.02, T:0.76
Consensus pattern (17 bp):
TATTTTTTTTCTTTTTC
Found at i:75504 original size:35 final size:36
Alignment explanation
Indices: 75437--75519 Score: 102
Period size: 35 Copynumber: 2.4 Consensus size: 36
75427 TTTTTTCTCA
*
75437 TTTTCTTTTT-TTTCTCATTTTCATTTTTTTCTTC-G
1 TTTTCTTTTTCTTTCTCATTTT-ATTTTCTTCTTCTG
*
75472 TTTTCTTTTTCTTTTTCTATTTT-TTTTCTTCTTCTG
1 TTTTCTTTTTCTTTCTC-ATTTTATTTTCTTCTTCTG
75508 TTTT-TTTTTCTT
1 TTTTCTTTTTCTT
75520 ATAATATATA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
35 28 0.65
36 10 0.23
37 5 0.12
ACGTcount: A:0.04, C:0.16, G:0.02, T:0.78
Consensus pattern (36 bp):
TTTTCTTTTTCTTTCTCATTTTATTTTCTTCTTCTG
Found at i:76385 original size:12 final size:13
Alignment explanation
Indices: 76363--76392 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
76353 GTAACCATTG
76363 TTGATATCACTTA
1 TTGATATCACTTA
76376 TTGA-ATCACTTA
1 TTGATATCACTTA
76388 TTGAT
1 TTGAT
76393 GATTTCACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.30, C:0.13, G:0.10, T:0.47
Consensus pattern (13 bp):
TTGATATCACTTA
Found at i:78315 original size:47 final size:45
Alignment explanation
Indices: 78241--78366 Score: 155
Period size: 47 Copynumber: 2.8 Consensus size: 45
78231 TATAAAATCT
*
78241 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * * *
78286 CTTACCATTTAAATTCCATAAGCTTGTAAGCTTATTTTTCCTATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
78333 CTTGCCA-TTATTCCGTAAGCTCATAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
78367 GCATGGTTAC
Statistics
Matches: 70, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
44 22 0.31
45 10 0.14
46 2 0.03
47 36 0.51
ACGTcount: A:0.29, C:0.22, G:0.08, T:0.40
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:78458 original size:40 final size:40
Alignment explanation
Indices: 78414--78520 Score: 205
Period size: 40 Copynumber: 2.7 Consensus size: 40
78404 ATAGCCAATA
78414 GCCCACCATATACACCGAAGTGTATTACACATAAGGTCGT
1 GCCCACCATATACACCGAAGTGTATTACACATAAGGTCGT
78454 GCCCACCATATACACCGAAGTGTATTACACATAAGGTCGT
1 GCCCACCATATACACCGAAGTGTATTACACATAAGGTCGT
*
78494 GCCCACCATATGCACCGAAGTGTATTA
1 GCCCACCATATACACCGAAGTGTATTA
78521 TAAACCTGCA
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
40 66 1.00
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.22
Consensus pattern (40 bp):
GCCCACCATATACACCGAAGTGTATTACACATAAGGTCGT
Found at i:82018 original size:112 final size:111
Alignment explanation
Indices: 81864--82285 Score: 565
Period size: 112 Copynumber: 3.8 Consensus size: 111
81854 TTTAATTTGC
* * * ** * *
81864 AGATATAATATTCTCTTCAGAAGAAGCAGAACAAATCCCTCTCTTCCAATATTTGATATTCCCTG
1 AGATCTAATATTCCCTTTA-AAGAAGTGGAACATATCCCTCTCTTCCAAGATTTGATATTCCCTG
* * * *
81929 AGTGACAGCGGAACACGTTTGCCTCGATTCAATGGATCAACTCCCCC
65 AGTGACAGCGGAACAAGTCTGCCCCGATTCAATGGATCAACTCCCCT
* * * * * **
81976 AGATCTGATATTACCTTTAGAAGAAGTGGAACATATCTCTCTCTTTCAATATTTGATATTCTTTG
1 AGATCTAATATTCCCTTTA-AAGAAGTGGAACATATCCCTCTCTTCCAAGATTTGATATTCCCTG
*
82041 AGTGACAGTGGAACAAGTCTGCCCCGATTCAATGGATCAACTCCCCT
65 AGTGACAGCGGAACAAGTCTGCCCCGATTCAATGGATCAACTCCCCT
*
82088 AGATCTAATATTCCCTTATAAAGAAGTGGAACAGATCCCTCTCTTCCAAGATTTGATATTCCCTG
1 AGATCTAATATTCCCTT-TAAAGAAGTGGAACATATCCCTCTCTTCCAAGATTTGATATTCCCTG
* *
82153 AGTGACAGCAGAACAAGTCTGCCCCGATTCAATGGATCAACTCCTCT
65 AGTGACAGCGGAACAAGTCTGCCCCGATTCAATGGATCAACTCCCCT
* ** *
82200 ATATCTAATATTCCCTTTTAAAGAAGTGGAACATATCTATCTCTTCTAAGATTTGATATTCCCTG
1 AGATCTAATATTCCC-TTTAAAGAAGTGGAACATATCCCTCTCTTCCAAGATTTGATATTCCCTG
*
82265 AGTGACAGCGGAATAAGTCTG
65 AGTGACAGCGGAACAAGTCTG
82286 TATCGATACC
Statistics
Matches: 273, Mismatches: 35, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
112 269 0.99
113 4 0.01
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31
Consensus pattern (111 bp):
AGATCTAATATTCCCTTTAAAGAAGTGGAACATATCCCTCTCTTCCAAGATTTGATATTCCCTGA
GTGACAGCGGAACAAGTCTGCCCCGATTCAATGGATCAACTCCCCT
Found at i:84350 original size:24 final size:24
Alignment explanation
Indices: 84314--84370 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
84304 GCATCTTGGA
*
84314 GTGATGAAGATGACTTCAATGATG
1 GTGATGAAGATGACTTCAAAGATG
*
84338 GTGATGAATATGACTTCAAAGATG
1 GTGATGAAGATGACTTCAAAGATG
*
84362 ATGATGAAG
1 GTGATGAAG
84371 TAGTCAACCT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.37, C:0.07, G:0.28, T:0.28
Consensus pattern (24 bp):
GTGATGAAGATGACTTCAAAGATG
Found at i:86550 original size:32 final size:33
Alignment explanation
Indices: 86512--86576 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 33
86502 TAAAGGGGTT
* *
86512 TTGGTTCTAGCTGAGCCT-TTAAAAGCTAGGGA
1 TTGGTTCTAGCTGAGCCTGTCAAAAACTAGGGA
* *
86544 TTGGTTCTAGTTTAGCCTGTCAAAAACTAGGGA
1 TTGGTTCTAGCTGAGCCTGTCAAAAACTAGGGA
86577 GTTATAAAGG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.32
Consensus pattern (33 bp):
TTGGTTCTAGCTGAGCCTGTCAAAAACTAGGGA
Found at i:89647 original size:65 final size:61
Alignment explanation
Indices: 89491--89647 Score: 161
Period size: 61 Copynumber: 2.5 Consensus size: 61
89481 GTAGTGCTAA
* * * * * * * *
89491 ACCTACACTAAGCTTACGCTCTAGTGCTAATCTGAATATGATACATAATGTTGTTCCCACT
1 ACCTACACTAGGTTTACACACTAGTGCTAATCTGAATATGACACATAAGGTTGTGCCCACC
* * * *
89552 GCCTACACTAGGTTTACACTCTAGTGCTAATCTGGATATGACACATAAGGTTGTGCCCTCC
1 ACCTACACTAGGTTTACACACTAGTGCTAATCTGAATATGACACATAAGGTTGTGCCCACC
*
89613 ACCTGCACTTAGTGTCCTTACACACTAGTGCTAAT
1 ACCTACAC-TAG-GT--TTACACACTAGTGCTAAT
89648 ATAAAACTAA
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
61 57 0.72
62 3 0.04
63 2 0.03
65 17 0.22
ACGTcount: A:0.27, C:0.26, G:0.16, T:0.31
Consensus pattern (61 bp):
ACCTACACTAGGTTTACACACTAGTGCTAATCTGAATATGACACATAAGGTTGTGCCCACC
Found at i:94914 original size:22 final size:22
Alignment explanation
Indices: 94886--94931 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
94876 CCGAAGTAAC
*
94886 ATTCATAACAAACATCATATAT
1 ATTCATAACAAAAATCATATAT
*
94908 ATTCATAATAAAAATCATATAT
1 ATTCATAACAAAAATCATATAT
94930 AT
1 AT
94932 ATATATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (22 bp):
ATTCATAACAAAAATCATATAT
Found at i:94931 original size:2 final size:2
Alignment explanation
Indices: 94924--94957 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
94914 AATAAAAATC
94924 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
94958 TCAACCTTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:98722 original size:32 final size:32
Alignment explanation
Indices: 98682--98848 Score: 174
Period size: 32 Copynumber: 5.2 Consensus size: 32
98672 TATAAATGGC
*
98682 ATACTGATTATACTATAG-ATTATCTGAATGCA
1 ATACTGATTCTACTAT-GCATTATCTGAATGCA
* * * * * **
98714 ATATTGATTCTATTGTGCATTATTTGACTATA
1 ATACTGATTCTACTATGCATTATCTGAATGCA
* * ** *
98746 ATATTGATTCTACTATGAAAAATCTGATTGCA
1 ATACTGATTCTACTATGCATTATCTGAATGCA
98778 ATACTGATTCTACTATGCATTATCTGAATGCA
1 ATACTGATTCTACTATGCATTATCTGAATGCA
* * *
98810 ATACCGATTCTACTATTCATTATATGAATGCA
1 ATACTGATTCTACTATGCATTATCTGAATGCA
98842 ATACTGA
1 ATACTGA
98849 ATCTGTTATG
Statistics
Matches: 108, Mismatches: 26, Indels: 2
0.79 0.19 0.01
Matches are distributed among these distances:
31 1 0.01
32 107 0.99
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.40
Consensus pattern (32 bp):
ATACTGATTCTACTATGCATTATCTGAATGCA
Done.